Shaun Mahony

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 29

Top Venues

Genome research

bioRxiv : the preprint server for biology

Nucleic acids research

Genome biology

Pennsylvania State University

National University of Ireland - Galway (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Pennsylvania State University Sep 01 2012

United States

Assistant Professor :: Biochemistry & Molecular Biology

Massachusetts Institute of Technology Aug 01 2007 - Aug 31 2012

United States

Research Scientist :: Computer Science and Artificial Intelligence Laboratory

University of Pittsburgh Jan 01 2006 - Jul 31 2007

United States

Postdoctoral Scholar :: Computational Biology

Education History

National University of Ireland - Galway Sep 01 2002 - Jan 01 2006

Ireland

PHD :: National Centre for Biomedical Engineering Science

Publications

Jianyu Yang, Kuangyu Yen, Shaun Mahony
Size-based expectation maximization for characterizing nucleosome positions and subtypes. Genome research (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research 34 (6) (2024)
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research 34 (6) (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research 34 (7) (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research 34 (6) (2024)
Jianyu Yang, Kuangyu Yen, Shaun Mahony
Size-based expectation maximization for characterizing nucleosome positions and subtypes. Genome research (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research 34 (7) (2024)
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research (2024)
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling, Tsu-Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic acids research (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome research (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research (2024)
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats. bioRxiv : the preprint server for biology (2023)
Sonny Arora, Jianyu Yang, Tomohiko Akiyama, Daniela James, Alexis Morrissey, Thomas R Blanda, Nitika Badjatia, William K M Lai, Minoru S H Ko, B Franklin Pugh, Shaun Mahony
Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin. bioRxiv : the preprint server for biology (2023)
Jianyu Yang, Kuangyu Yen, Shaun Mahony
SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes. bioRxiv : the preprint server for biology (2023)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Weaver, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv : the preprint server for biology (2023)
Kelly Cochran, Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross Cameron Hardison, Anshul Kundaje, Shaun Mahony
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding. Genome research 32 (3) (2022)
Danying Shao, Gretta D Kellogg, Ali Nematbakhsh, Prashant K Kuntala, Shaun Mahony, B Franklin Pugh, William K M Lai
PEGR: a flexible management platform for reproducible epigenomic and genomic research. Genome biology 23 (1) (2022)
Sudarshan Pinglay, Milica Bulajić, Dylan P Rahe, Emily Huang, Ran Brosh, Nicholas E Mamrak, Benjamin R King, Sergei German, John A Cadley, Lila Rieber, Nicole Easo, Timothée Lionnet, Shaun Mahony, Matthew T Maurano, Liam J Holt, Esteban Orlando Mazzoni, Jef D Boeke
Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science (New York, N.Y.) 377 (6601) (2022)
Divyanshi Srivastava, Begüm Aydin, Esteban O Mazzoni, Shaun Mahony
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding. Genome biology 22 (1) (2021)
Milica Bulajić, Divyanshi Srivastava, Jeremy S Dasen, Hynek Wichterle, Shaun Mahony, Esteban Orlando Mazzoni
Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns. Development (Cambridge, England) 147 (22) (2020)
Guanjue Xiang, Cheryl A Keller, Elisabeth F Heuston, Belinda M Giardine, Lin An, Alexander Q Wixom, Amber Miller, April Cockburn, Michael E G Sauria, Kathryn Weaver, Jens Lichtenberg, Berthold Göttgens, Qunhua Li, David Bodine, Shaun Mahony, James Taylor, Gerd A Blobel, Mitchell J Weiss, Yong Cheng, Feng Yue, Jim R Hughes, Douglas R Higgs, Yu Zhang, Ross Cameron Hardison
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome research 30 (3) (2020)
Lila Rieber, Shaun Mahony
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types. Epigenetics & chromatin 12 (1) (2019)
Begüm Aydin, Akshay Kakumanu, Mary Rossillo, Mireia Moreno-Estellés, Görkem Garipler, Niels Ringstad, Nuria Flames, Shaun Mahony, Esteban Orlando Mazzoni
Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes. Nature neuroscience 22 (6) (2019)
Yu Zhang, Shaun Mahony
Direct prediction of regulatory elements from partial data without imputation. PLoS computational biology 15 (11) (2019)
Akshay Kakumanu, Silvia Velasco, Esteban Mazzoni, Shaun Mahony
Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLoS computational biology 13 (10) (2017)
Simona Lodato, Bradley J Molyneaux, Emanuela Zuccaro, Loyal A Goff, Hsu-Hsin Chen, Wen Yuan, Alyssa Meleski, Emi Takahashi, Shaun Mahony, John L Rinn, David K Gifford, Paola Arlotta
Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nature neuroscience 17 (8) (2014)

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Publication Activity (10 Years)

Top Topics

Top Venues

Shaun Mahony